Slartibartfast

Couldn't be too hard, right? Pull a second brake lever from the junkyard, make some sort of bracket to fit the two (if you pulled the rubber trim out of the console, they might both fit w/o trimming anything), then run the cables to where the splitter used to be... then take it to a shop and ask them to check your brakes, and watch the tech guys try to figure it out.

There's no way around it. That is one ugly Pathy. Ten-speaker Bose sounds pretty nice, though.

Long drill bit?

Start click is pretty common, there's a solenoid in the starter that can get iffy. Or, your starter contacts may be dirty/corroded; given the mud (I hope that's mud) in your pics, you could easily just have dirty terminals. Clean them up, screw them back in, see if that helps. If you can, clean up the engine bay a bit. It'll make working on it a lot easier.

Deleting it entirely could cause problems with the emissions test. That would be something to check beforehand. Also I think it would turn on a check light or put up a code, and IIRC you won't pass emissions with a code or a light on. (My area doesn't do smog checks, so this is secondhand info.) From what I've read (Wikipedia), the EGR is controlled by vacuum from the intake (which you didn't tinker with, shouldn't be a problem). It channels some exhaust to the intake to suppress NOx emissions. So, lower back pressure would decrease the amount of gas going through the valve (same opening, less pressure), but I don't know if it would be enough to make a difference. Also, EGR (again according to Wikipedia) is turned off at idle (where it would cause choppiness) and under high load (where it would decrease peak power). If you're trying to see it work, revving it may not be enough; it may require actual driving. Short of running test leads through the firewall/vents/out the window, or having a friend ride the front bumper with a voltmeter, I'm not sure how you'd test its operation. But, again, an exhaust job shouldn't change how the valve opens. This is what I'm looking at: http://en.wikipedia.org/wiki/Exhaust_gas_recirculation

I washed the bird crap off, replaced a front marker light (NEVER wash a plastic lens with alcohol, learned the hard way), and gave up trying to remember which position on the hatch lock did what.

Looks like it'll work. The little seatbelt clips on mine were busted, so I just made new ones out of wire. The stock bits break really easily, especially when someone gets in the back seat and doesn't know how they work.

Ammeter maybe? Although, if you had an altimeter, and your electrical system was pulsing, it would probably bounce around too. If it's not tied to RPM, then I don't see how your alternator would cause it. Check the voltage regulator? Is it a steady flash, or a flicker?

That's what we did then the floors in mine needed doing, just had the junkyard guys cut a floor section. Went right in. Mine wasn't rotted nearly as bad though, so we didn't have as much to hack out. It looks like you've got a bit of sheet metal still holding the hold down in place, so why not leave it (or at least one bolt if the end is rotten) in place, put your flat floor in, and then build up as necessary to secure the hold down? It should work okay without it, but I imagine it might rattle around a bit.

^Building on what he said, I've read that Pathy starting problems are sometimes due to the ignition switch not having the power to engage the starter solenoid. If you wire your ignition through another relay (so that your starter and starter solenoid get power directly from the battery), this apparently makes them more likely to start (rather than just clicking). So perhaps the battery was a little too low to engage the starter solenoid when they tried it, but when you tried it, the battery had regrouped a bit and was able to flip the solenoid? I read about the relay hack here: http://www.4x4parts.com/ubbthreads/showflat.php?Cat=0&Number=315995&an=&page=0&vc=1 (Keep in mind that I'm a noob, and this could be total crap.)

From what I've heard, the FJ's go through a lot of windshields as well... they're nearly vertical, so there's little room for deflection. My dad had an Xterra (don't remember what year, probably the first) for a while, and while it was a good truck in general, it was gutless. Pretty sure they fixed that for the next model year though.

Have a friend drive it, ride shotgun, and push on various panels until it stops rattling. If nothing else, you'll get a better idea of where the rattle is (you can home in on it without worrying about going off the road).

Look up pictures of the individual parts, both the OEM and your intended replacement. Look for markings, mounts, etc. There may be obvious differences. If not, it may be the same mount, or at least close enough to fake it. Sometimes I suspect there's a group of engineers at Nissan who just change things at random to look busy. Example: I pulled a tail light and a rear fender flare from a 93, to put on my 95 (same body style). The tail light fit, but the flare had totally different mounts that didn't line up with my sheet metal. Then again, yours is newer than mine, maybe they'd all retired by then.

The reason for putting the filter after the coolers is probably that the filter is designed to protect the trans, not the coolers. If there's gunk in the coolers, and it comes loose (think heart attack commercials), better to have the filter grab it up. Of course, whatever was in the coolers was going through the trans before, and hadn't made it explode... so... meh. If your trans is making enough crud for the filter placement to matter, filter placement is the least of your problems.

If this is what I'm thinking of (tar-like substance holding down the padding under the carpets), heat and scrape will take forever and you'll still have some left over. You'd probably get it out faster/better with the dry ice. Just don't asphyxiate yourself. It's still soft in my 95, at least under the carpet on the rear wheel wells. Maybe it hardens up given another four years? Or maybe they used different stuff?

That... sounds like something to sort out ASAP. I'd check under it first and make sure that the grease monkeys who aligned it put all the screws back in. My uneducated guess is that something is really loose somewhere, and when the truck tilts forward at the stoplight (from braking), or when you get on the gas again, something shifts around. Does it clunk at all when it does this? I've heard of the rear end shifting around a bit and making the car veer if the rear suspension bushings are hosed, but IIRC that was just when it hit bumps. Also, maybe check the bolt on the steering arm?

Sounds like the MAF has a vacuum leak, and you're probably right about it having some dirt in there. You may have dislodged something when you took the airbox apart. Clean it out however you can (suck the screen end with a shop-vac? A little duct tape should seal the hose to it) and try it again. It may just be worn out, like a plunger or a seal or something going bad and letting air whistle past, but I'd expect that to be more gradual. But yeah, if you can't get it figured, try a different MAF.

Sounds like a bad battery, bad alternator, or a wiring problem. The bonehead in me says clean the battery top, the posts, and the cables, and check the levels (if it's that kind of battery). The battery could conceivably be losing power through dirty connections or trickling power through grime between the poles. Can't hurt, right? But I doubt it's your problem. Put the battery on a trickle charger until it's at full voltage. If that clears it up for a while, maybe it's just not getting charged properly from the engine. If it's not getting charge, that suggests a problem with your alternator, or the wiring between the alternator and the battery. I guess it could be the belt but I'll bet you'd hear it squealing if it was slipping. If trickle charging doesn't help, it's your battery, though your alternator could still be responsible (killing the battery by overcharging and venting electrolyte). If the electrolyte looks fine, your alternator probably isn't to blame, and the battery's just worn out. Or, you left the dome light on.

Or just make yourself a little smoke bomb, put it in a Coke can, and set it off. Much cheaper.

Glad you got it figured.

When my uncle welded up the holes in mine, he went all the way around (spot and fill) with no sealer, except for the undercoating I'll be putting on soon. We used floor bits cut from a wrecked 93 at the local yard (cut a bit bigger than the holes for overlap). He used the wirefeed he uses for everything from thin sheets to frame steel. The patch wasn't cheap, but it looks good. One thing to look out for, the old undercoating (unless yours has all fallen off) will try to catch fire from the weld heat. We put a hose underneath the truck with a sprinkler sort of thing on the end to keep it cool under there. (Luckily the seatbelt mounts and all were fine, so we left them alone. Since we were cutting bits from a wrecked Pathy anyway, we would've just taken the brackets out.)

Tore it apart to put new belts in, only to find that the auto parts place gave us the wrong belts.

All I can think of is that you've got a bad harness to your new stereo, or the stereo itself is screwy. While direct-wiring your amp may not be a bad idea, doesn't sound like that's the problem. Definitely do the speaker test... if it fails, sounds like your new stereo is a paperweight. Just curious, what kind of stereo? I put an xplod in mine, no issues.

Take the following with a grain of salt, as I didn't even know what a swirl valve was until today. According to this http://forums.nicoclub.com/swirl-valve-control-solenoid-p1130-t339097.html, a little crud in the vacuum line keeps the actuator from working right, and generates an error code. Clean the hose, and, apparently, problem solved. I'd expect a solenoid to have a return spring, but it may rely on vacuum, airflow, or something else for this. Hopefully it's just your vac line, as these are apparently a PITA to get except from the dealer, and they'll charge you just to open the hood. Hope that helps, gotta love Google.

IIRC, there is an amplifier fuse in the fuse box. It may be blown out/missing. (Did the old stereo work before you pulled it?) Also, I have to ask... is the volume off on the radio? I only ask because that's the kind of herp derp I generally pull. Mine has some speaker hiss when it's on but not playing (aux mode w/o iPod attached). If your speakers are hissing, the amp isn't getting signal. If they're totally dead, the amp isn't getting power.